Multiple sequence alignment - TraesCS6B01G241400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G241400 chr6B 100.000 2282 0 0 1 2282 423094572 423092291 0.000000e+00 4215.0
1 TraesCS6B01G241400 chr1A 96.154 2314 31 7 1 2282 508961025 508963312 0.000000e+00 3727.0
2 TraesCS6B01G241400 chr1A 88.579 359 15 8 1580 1920 232346816 232346466 1.630000e-111 412.0
3 TraesCS6B01G241400 chr1A 94.286 140 6 2 2129 2268 562935012 562935149 1.780000e-51 213.0
4 TraesCS6B01G241400 chr1B 94.017 2106 85 21 1 2075 167564593 167562498 0.000000e+00 3153.0
5 TraesCS6B01G241400 chr6A 96.319 1766 36 6 1 1738 26327180 26328944 0.000000e+00 2874.0
6 TraesCS6B01G241400 chr6A 92.910 536 9 12 1776 2282 26328937 26329472 0.000000e+00 752.0
7 TraesCS6B01G241400 chr3A 97.699 1521 31 3 558 2075 411269752 411271271 0.000000e+00 2612.0
8 TraesCS6B01G241400 chr3A 93.561 497 22 2 1577 2071 193870392 193870880 0.000000e+00 732.0
9 TraesCS6B01G241400 chr3A 96.104 154 5 1 2129 2282 30183206 30183054 1.350000e-62 250.0
10 TraesCS6B01G241400 chr3A 94.286 140 6 2 2129 2268 235349110 235348973 1.780000e-51 213.0
11 TraesCS6B01G241400 chr3A 100.000 44 0 0 2078 2121 411271562 411271605 5.220000e-12 82.4
12 TraesCS6B01G241400 chr6D 95.945 1233 42 5 1 1229 79981697 79980469 0.000000e+00 1993.0
13 TraesCS6B01G241400 chr5A 93.698 1333 52 12 3 1329 510201365 510200059 0.000000e+00 1967.0
14 TraesCS6B01G241400 chr5A 89.116 1369 125 15 1 1354 296676598 296675239 0.000000e+00 1681.0
15 TraesCS6B01G241400 chr5A 93.084 535 26 3 1489 2020 510199558 510199032 0.000000e+00 773.0
16 TraesCS6B01G241400 chr7D 93.277 1309 64 12 1 1305 114143635 114142347 0.000000e+00 1908.0
17 TraesCS6B01G241400 chr2A 92.663 1213 76 9 102 1308 355588703 355587498 0.000000e+00 1735.0
18 TraesCS6B01G241400 chr2A 93.688 301 18 1 1189 1488 467111708 467112008 1.240000e-122 449.0
19 TraesCS6B01G241400 chr4B 95.227 838 25 10 1245 2075 494950350 494951179 0.000000e+00 1312.0
20 TraesCS6B01G241400 chr1D 93.562 699 26 4 1064 1761 493748845 493748165 0.000000e+00 1024.0
21 TraesCS6B01G241400 chr1D 95.618 251 8 2 1827 2075 493748158 493747909 1.270000e-107 399.0
22 TraesCS6B01G241400 chr1D 100.000 44 0 0 2078 2121 493747620 493747577 5.220000e-12 82.4
23 TraesCS6B01G241400 chr5B 90.426 564 28 9 1521 2066 397291813 397292368 0.000000e+00 719.0
24 TraesCS6B01G241400 chr7B 87.617 533 32 13 1376 1886 547961919 547962439 2.530000e-164 588.0
25 TraesCS6B01G241400 chr7B 83.019 159 11 11 2120 2273 648276983 648276836 1.840000e-26 130.0
26 TraesCS6B01G241400 chr5D 88.462 416 32 12 1515 1920 320239231 320238822 2.630000e-134 488.0
27 TraesCS6B01G241400 chr5D 95.597 159 2 4 2128 2281 395177772 395177614 1.350000e-62 250.0
28 TraesCS6B01G241400 chr5D 91.503 153 5 2 2129 2281 382015032 382015176 1.070000e-48 204.0
29 TraesCS6B01G241400 chr3B 91.379 348 15 4 1163 1506 597105100 597105436 1.600000e-126 462.0
30 TraesCS6B01G241400 chr3B 96.078 51 0 2 1489 1539 158150122 158150074 5.220000e-12 82.4
31 TraesCS6B01G241400 chr4D 98.077 156 1 2 2128 2282 124257337 124257491 1.040000e-68 270.0
32 TraesCS6B01G241400 chr2D 97.297 37 1 0 2079 2115 13209564 13209528 1.890000e-06 63.9
33 TraesCS6B01G241400 chr3D 100.000 32 0 0 2084 2115 168502846 168502815 2.450000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G241400 chr6B 423092291 423094572 2281 True 4215.0 4215 100.000000 1 2282 1 chr6B.!!$R1 2281
1 TraesCS6B01G241400 chr1A 508961025 508963312 2287 False 3727.0 3727 96.154000 1 2282 1 chr1A.!!$F1 2281
2 TraesCS6B01G241400 chr1B 167562498 167564593 2095 True 3153.0 3153 94.017000 1 2075 1 chr1B.!!$R1 2074
3 TraesCS6B01G241400 chr6A 26327180 26329472 2292 False 1813.0 2874 94.614500 1 2282 2 chr6A.!!$F1 2281
4 TraesCS6B01G241400 chr3A 411269752 411271605 1853 False 1347.2 2612 98.849500 558 2121 2 chr3A.!!$F2 1563
5 TraesCS6B01G241400 chr6D 79980469 79981697 1228 True 1993.0 1993 95.945000 1 1229 1 chr6D.!!$R1 1228
6 TraesCS6B01G241400 chr5A 296675239 296676598 1359 True 1681.0 1681 89.116000 1 1354 1 chr5A.!!$R1 1353
7 TraesCS6B01G241400 chr5A 510199032 510201365 2333 True 1370.0 1967 93.391000 3 2020 2 chr5A.!!$R2 2017
8 TraesCS6B01G241400 chr7D 114142347 114143635 1288 True 1908.0 1908 93.277000 1 1305 1 chr7D.!!$R1 1304
9 TraesCS6B01G241400 chr2A 355587498 355588703 1205 True 1735.0 1735 92.663000 102 1308 1 chr2A.!!$R1 1206
10 TraesCS6B01G241400 chr4B 494950350 494951179 829 False 1312.0 1312 95.227000 1245 2075 1 chr4B.!!$F1 830
11 TraesCS6B01G241400 chr1D 493747577 493748845 1268 True 501.8 1024 96.393333 1064 2121 3 chr1D.!!$R1 1057
12 TraesCS6B01G241400 chr5B 397291813 397292368 555 False 719.0 719 90.426000 1521 2066 1 chr5B.!!$F1 545
13 TraesCS6B01G241400 chr7B 547961919 547962439 520 False 588.0 588 87.617000 1376 1886 1 chr7B.!!$F1 510

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
980 985 1.068352 AAGGCTTGAGGGTCTTGGGT 61.068 55.0 0.0 0.0 29.29 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2763 1.406341 GCCCGTGTTTCCACTGCTATA 60.406 52.381 0.0 0.0 39.55 1.31 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 6.943718 GGTCTACTATTAGATCACTAGCCTGT 59.056 42.308 0.00 0.00 35.71 4.00
202 204 9.573133 GATAGGATGAATTTTTGTTTGTCGATT 57.427 29.630 0.00 0.00 0.00 3.34
203 205 9.927668 ATAGGATGAATTTTTGTTTGTCGATTT 57.072 25.926 0.00 0.00 0.00 2.17
221 223 4.744137 CGATTTTTGATGAGGCAACAACAA 59.256 37.500 4.07 4.07 41.41 2.83
532 537 6.702329 AGAGACAAAGTCAATAAAGGTCGAT 58.298 36.000 0.00 0.00 34.60 3.59
695 700 1.593196 AGCAGCTGTCGCAAAAACTA 58.407 45.000 16.64 0.00 39.10 2.24
834 839 4.037923 ACAAGACCTTATTGCAGGTGTTTG 59.962 41.667 0.00 7.42 45.91 2.93
924 929 1.485895 TGAGATCATGAACCATGCGGA 59.514 47.619 0.00 0.00 41.18 5.54
980 985 1.068352 AAGGCTTGAGGGTCTTGGGT 61.068 55.000 0.00 0.00 29.29 4.51
1101 1112 2.932622 GCTTGAGATGAGGCTTGTTCGA 60.933 50.000 0.00 0.00 0.00 3.71
1116 1127 4.192429 TGTTCGAATGCTTGAGATGAGA 57.808 40.909 0.00 0.00 0.00 3.27
1182 1233 0.169009 GGCTTGTTCCGATGCTTGAC 59.831 55.000 0.00 0.00 0.00 3.18
1195 1246 1.881973 TGCTTGACATGAGGCTTGTTC 59.118 47.619 0.00 0.00 0.00 3.18
1208 1259 3.015327 GGCTTGTTCAGATGCTTGAGAT 58.985 45.455 0.00 0.00 0.00 2.75
1211 1262 4.201832 GCTTGTTCAGATGCTTGAGATGAG 60.202 45.833 0.00 0.00 0.00 2.90
1213 1264 2.613133 GTTCAGATGCTTGAGATGAGGC 59.387 50.000 0.00 0.00 0.00 4.70
1214 1265 2.117051 TCAGATGCTTGAGATGAGGCT 58.883 47.619 0.00 0.00 0.00 4.58
1215 1266 2.504585 TCAGATGCTTGAGATGAGGCTT 59.495 45.455 0.00 0.00 0.00 4.35
1216 1267 2.614520 CAGATGCTTGAGATGAGGCTTG 59.385 50.000 0.00 0.00 0.00 4.01
1217 1268 2.239150 AGATGCTTGAGATGAGGCTTGT 59.761 45.455 0.00 0.00 0.00 3.16
1218 1269 2.574006 TGCTTGAGATGAGGCTTGTT 57.426 45.000 0.00 0.00 0.00 2.83
1219 1270 2.430465 TGCTTGAGATGAGGCTTGTTC 58.570 47.619 0.00 0.00 0.00 3.18
1220 1271 1.742268 GCTTGAGATGAGGCTTGTTCC 59.258 52.381 0.00 0.00 0.00 3.62
1221 1272 2.005451 CTTGAGATGAGGCTTGTTCCG 58.995 52.381 0.00 0.00 0.00 4.30
1222 1273 1.266178 TGAGATGAGGCTTGTTCCGA 58.734 50.000 0.00 0.00 0.00 4.55
1223 1274 1.833630 TGAGATGAGGCTTGTTCCGAT 59.166 47.619 0.00 0.00 0.00 4.18
1224 1275 2.237143 TGAGATGAGGCTTGTTCCGATT 59.763 45.455 0.00 0.00 0.00 3.34
1225 1276 2.869192 GAGATGAGGCTTGTTCCGATTC 59.131 50.000 0.00 0.00 0.00 2.52
1226 1277 2.503356 AGATGAGGCTTGTTCCGATTCT 59.497 45.455 0.00 0.00 0.00 2.40
1227 1278 2.859165 TGAGGCTTGTTCCGATTCTT 57.141 45.000 0.00 0.00 0.00 2.52
1228 1279 2.426522 TGAGGCTTGTTCCGATTCTTG 58.573 47.619 0.00 0.00 0.00 3.02
1229 1280 2.038426 TGAGGCTTGTTCCGATTCTTGA 59.962 45.455 0.00 0.00 0.00 3.02
1230 1281 2.416893 GAGGCTTGTTCCGATTCTTGAC 59.583 50.000 0.00 0.00 0.00 3.18
1231 1282 2.151202 GGCTTGTTCCGATTCTTGACA 58.849 47.619 0.00 0.00 0.00 3.58
1232 1283 2.749621 GGCTTGTTCCGATTCTTGACAT 59.250 45.455 0.00 0.00 0.00 3.06
1233 1284 3.426695 GGCTTGTTCCGATTCTTGACATG 60.427 47.826 0.00 0.00 0.00 3.21
1234 1285 3.436704 GCTTGTTCCGATTCTTGACATGA 59.563 43.478 0.00 0.00 0.00 3.07
1235 1286 4.436584 GCTTGTTCCGATTCTTGACATGAG 60.437 45.833 0.00 0.00 0.00 2.90
1236 1287 3.599343 TGTTCCGATTCTTGACATGAGG 58.401 45.455 0.00 0.00 0.00 3.86
1237 1288 2.315925 TCCGATTCTTGACATGAGGC 57.684 50.000 0.00 0.00 0.00 4.70
1238 1289 1.833630 TCCGATTCTTGACATGAGGCT 59.166 47.619 0.00 0.00 0.00 4.58
1239 1290 2.237143 TCCGATTCTTGACATGAGGCTT 59.763 45.455 0.00 0.00 0.00 4.35
1240 1291 2.353889 CCGATTCTTGACATGAGGCTTG 59.646 50.000 0.00 0.00 0.00 4.01
1241 1292 3.005554 CGATTCTTGACATGAGGCTTGT 58.994 45.455 0.00 0.00 0.00 3.16
1242 1293 3.438087 CGATTCTTGACATGAGGCTTGTT 59.562 43.478 0.00 0.00 0.00 2.83
1243 1294 4.436584 CGATTCTTGACATGAGGCTTGTTC 60.437 45.833 0.00 0.00 0.00 3.18
1425 1818 4.968259 TGTGAGGCTTGTATGTGTAACTT 58.032 39.130 0.00 0.00 38.04 2.66
1726 2324 4.998051 AGAAGAGAGAAGAGAAGTCCTGT 58.002 43.478 0.00 0.00 0.00 4.00
2147 3123 7.791029 ACTGAAAAGAGAAGAGAAAGAGAAGT 58.209 34.615 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 3.116096 AGTAGGCTACATCCCAGTTGA 57.884 47.619 25.48 0.0 0.00 3.18
202 204 4.462508 TGTTGTTGTTGCCTCATCAAAA 57.537 36.364 4.20 0.0 31.68 2.44
203 205 4.081752 AGTTGTTGTTGTTGCCTCATCAAA 60.082 37.500 4.20 0.0 31.68 2.69
221 223 0.396811 AACTTAGGCCTCGCAGTTGT 59.603 50.000 9.68 0.0 0.00 3.32
532 537 5.046304 CAGGAACTCCCTCATCACTTTTCTA 60.046 44.000 0.00 0.0 45.60 2.10
695 700 9.862371 CTGTTGTACTAATCTAATGTCAAGTCT 57.138 33.333 0.00 0.0 0.00 3.24
834 839 4.170468 TCATAGCCTTCAAATTCCTCCC 57.830 45.455 0.00 0.0 0.00 4.30
924 929 6.987557 TGTGGTATTTTATACCCATTTCCCT 58.012 36.000 12.14 0.0 36.79 4.20
980 985 4.099573 GCATGTTAGTCTTGGAGGTAGCTA 59.900 45.833 0.00 0.0 0.00 3.32
1101 1112 4.699257 GGAACAAGTCTCATCTCAAGCATT 59.301 41.667 0.00 0.0 0.00 3.56
1116 1127 2.254546 TGTCAAGCATCGGAACAAGT 57.745 45.000 0.00 0.0 0.00 3.16
1182 1233 2.366533 AGCATCTGAACAAGCCTCATG 58.633 47.619 0.00 0.0 0.00 3.07
1195 1246 2.614520 CAAGCCTCATCTCAAGCATCTG 59.385 50.000 0.00 0.0 0.00 2.90
1208 1259 2.038426 TCAAGAATCGGAACAAGCCTCA 59.962 45.455 0.00 0.0 0.00 3.86
1211 1262 2.151202 TGTCAAGAATCGGAACAAGCC 58.849 47.619 0.00 0.0 0.00 4.35
1213 1264 4.093998 CCTCATGTCAAGAATCGGAACAAG 59.906 45.833 0.00 0.0 0.00 3.16
1214 1265 4.002982 CCTCATGTCAAGAATCGGAACAA 58.997 43.478 0.00 0.0 0.00 2.83
1215 1266 3.599343 CCTCATGTCAAGAATCGGAACA 58.401 45.455 0.00 0.0 0.00 3.18
1216 1267 2.352960 GCCTCATGTCAAGAATCGGAAC 59.647 50.000 0.00 0.0 0.00 3.62
1217 1268 2.237143 AGCCTCATGTCAAGAATCGGAA 59.763 45.455 0.00 0.0 0.00 4.30
1218 1269 1.833630 AGCCTCATGTCAAGAATCGGA 59.166 47.619 0.00 0.0 0.00 4.55
1219 1270 2.322355 AGCCTCATGTCAAGAATCGG 57.678 50.000 0.00 0.0 0.00 4.18
1220 1271 3.005554 ACAAGCCTCATGTCAAGAATCG 58.994 45.455 0.00 0.0 0.00 3.34
1221 1272 4.456911 TGAACAAGCCTCATGTCAAGAATC 59.543 41.667 0.00 0.0 0.00 2.52
1222 1273 4.401022 TGAACAAGCCTCATGTCAAGAAT 58.599 39.130 0.00 0.0 0.00 2.40
1223 1274 3.817084 CTGAACAAGCCTCATGTCAAGAA 59.183 43.478 0.00 0.0 0.00 2.52
1224 1275 3.071457 TCTGAACAAGCCTCATGTCAAGA 59.929 43.478 0.00 0.0 0.00 3.02
1225 1276 3.405831 TCTGAACAAGCCTCATGTCAAG 58.594 45.455 0.00 0.0 0.00 3.02
1226 1277 3.490439 TCTGAACAAGCCTCATGTCAA 57.510 42.857 0.00 0.0 0.00 3.18
1227 1278 3.340928 CATCTGAACAAGCCTCATGTCA 58.659 45.455 0.00 0.0 0.00 3.58
1228 1279 2.097142 GCATCTGAACAAGCCTCATGTC 59.903 50.000 0.00 0.0 0.00 3.06
1229 1280 2.089980 GCATCTGAACAAGCCTCATGT 58.910 47.619 0.00 0.0 0.00 3.21
1230 1281 2.366533 AGCATCTGAACAAGCCTCATG 58.633 47.619 0.00 0.0 0.00 3.07
1231 1282 2.753452 CAAGCATCTGAACAAGCCTCAT 59.247 45.455 0.00 0.0 0.00 2.90
1232 1283 2.156917 CAAGCATCTGAACAAGCCTCA 58.843 47.619 0.00 0.0 0.00 3.86
1233 1284 2.419324 CTCAAGCATCTGAACAAGCCTC 59.581 50.000 0.00 0.0 0.00 4.70
1234 1285 2.039480 TCTCAAGCATCTGAACAAGCCT 59.961 45.455 0.00 0.0 0.00 4.58
1235 1286 2.430465 TCTCAAGCATCTGAACAAGCC 58.570 47.619 0.00 0.0 0.00 4.35
1236 1287 3.688185 TCATCTCAAGCATCTGAACAAGC 59.312 43.478 0.00 0.0 0.00 4.01
1237 1288 4.201832 GCTCATCTCAAGCATCTGAACAAG 60.202 45.833 0.00 0.0 39.61 3.16
1238 1289 3.688185 GCTCATCTCAAGCATCTGAACAA 59.312 43.478 0.00 0.0 39.61 2.83
1239 1290 3.055312 AGCTCATCTCAAGCATCTGAACA 60.055 43.478 0.00 0.0 42.35 3.18
1240 1291 3.533547 AGCTCATCTCAAGCATCTGAAC 58.466 45.455 0.00 0.0 42.35 3.18
1241 1292 3.908643 AGCTCATCTCAAGCATCTGAA 57.091 42.857 0.00 0.0 42.35 3.02
1242 1293 3.055312 ACAAGCTCATCTCAAGCATCTGA 60.055 43.478 0.00 0.0 42.35 3.27
1243 1294 3.271729 ACAAGCTCATCTCAAGCATCTG 58.728 45.455 0.00 0.0 42.35 2.90
2075 2763 1.406341 GCCCGTGTTTCCACTGCTATA 60.406 52.381 0.00 0.0 39.55 1.31
2147 3123 3.066291 ACTCTCGCTCTCTTCTCTTCA 57.934 47.619 0.00 0.0 0.00 3.02


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.